Contacts of the helix formed by residues 482 - 493 (chain C) in PDB entry 5ZR1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 482 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476C THR 4.6 2.2 + - - -
480C PHE 3.7 1.8 + - - -
481C PRO* 1.3 68.9 - - - +
483C TYR* 1.3 61.5 + - - +
484C LYS 3.6 1.3 - - - -
485C SER* 3.8 22.2 - - - -
486C ASN* 2.8 37.1 + - - +
415E LYS* 4.4 16.7 - - - +
416E ALA 4.3 2.0 - - - -
417E ASN* 3.8 20.6 - - - +
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Residues in contact with TYR 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.7 9.6 - - + -
317B TYR* 3.5 48.0 - + + +
456B THR* 2.7 30.3 + - - -
457B ASP 4.9 0.5 - - - -
458B HIS 3.4 26.7 + - - -
459B ILE* 3.5 23.3 - - - -
461B ALA* 3.6 5.7 - - + +
462B PRO* 3.5 32.8 - - + -
477B PHE* 5.0 1.1 - + - -
481C PRO* 2.9 8.9 + - + -
482C SER* 1.3 74.3 - - - +
484C LYS* 1.3 64.1 + - - +
486C ASN* 3.2 12.5 + - - +
487C ILE* 3.3 24.5 + - + +
416E ALA 4.1 6.8 + - - +
417E ASN 5.3 0.7 - - - +
418E ILE* 4.0 18.6 - - + +
421E PHE* 5.6 2.2 - + + -
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Residues in contact with LYS 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 3.7 29.8 - - + +
460B TYR* 4.3 16.2 - - + -
483C TYR* 1.3 81.3 - - + +
485C SER* 1.3 60.8 + - - +
487C ILE* 2.9 17.2 + - - +
488C GLU* 2.9 41.1 + - - +
612C VAL* 4.3 11.0 - - - +
613C TRP 3.4 15.8 + - - -
616C ILE* 2.6 33.6 + - - +
384E GLU* 4.4 6.2 + - - -
387E LEU* 4.8 3.4 - - + -
416E ALA* 4.0 16.4 + - + +
421E PHE* 3.8 28.3 - - + -
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Residues in contact with SER 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C SER* 3.7 20.1 + - - -
483C TYR 3.3 0.6 - - - -
484C LYS* 1.3 80.6 - - - +
486C ASN* 1.3 58.3 + - - +
488C GLU* 3.4 11.1 + - - +
489C ASP* 2.9 40.6 + - - +
615C GLY 5.0 3.5 + - - -
616C ILE* 4.4 9.5 + - - -
415E LYS* 3.3 38.0 - - - +
416E ALA 4.8 1.2 + - - -
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Residues in contact with ASN 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TYR* 3.2 24.3 + - + -
479B ASP* 4.2 7.2 - - - +
477C GLN* 3.1 33.4 + - - +
482C SER* 2.8 36.6 + - - +
483C TYR 3.6 5.8 - - - +
484C LYS 3.2 0.2 - - - -
485C SER* 1.3 76.5 - - - +
487C ILE* 1.3 57.4 + - - +
489C ASP* 4.1 7.1 - - - +
490C ASN* 2.6 38.4 + - - +
401F LYS* 5.6 4.1 + - - +
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Residues in contact with ILE 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TYR* 3.7 28.7 - - + -
318B GLY* 3.8 25.8 - - - +
319B VAL* 4.9 8.9 - - + +
457B ASP 5.9 4.5 - - - +
459B ILE* 3.9 28.0 - - + -
479B ASP* 4.6 0.2 - - - +
483C TYR* 3.3 22.2 - - + +
484C LYS* 2.9 12.2 + - - +
486C ASN* 1.3 79.0 - - - +
488C GLU* 1.3 59.7 + - - +
489C ASP 3.3 0.2 - - - -
490C ASN* 3.4 5.6 + - - +
491C LEU* 3.0 40.6 + - + +
594C MET* 5.3 8.7 - - + -
596C LEU* 5.8 0.2 - - + -
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Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 3.4 12.8 - - + +
484C LYS* 2.9 54.2 + - - +
485C SER* 3.4 13.4 + - - +
487C ILE* 1.3 75.4 - - - +
489C ASP* 1.3 62.1 + - - +
491C LEU* 4.2 8.3 - - + -
492C LEU* 2.9 32.2 + - - +
525C PHE* 3.8 25.3 - - + -
596C LEU* 5.7 0.2 - - + -
612C VAL* 3.3 20.0 - - + +
614C ARG* 3.9 32.4 + - + +
615C GLY 4.1 3.8 + - - -
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Residues in contact with ASP 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C SER* 2.9 29.6 + - - +
486C ASN* 4.5 8.8 - - - +
488C GLU* 1.3 77.3 - - - +
490C ASN* 1.3 60.6 + - - +
492C LEU* 4.8 0.2 - - - -
493C SER* 3.0 38.9 + - - +
496C GLN* 5.1 2.3 + - - +
614C ARG* 2.9 37.8 + - - +
415E LYS* 6.2 0.2 - - - -
401F LYS* 5.2 6.5 - - - +
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Residues in contact with ASN 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLY* 5.1 0.6 - - - -
319B VAL* 3.8 12.3 - - + -
479B ASP* 3.2 18.8 + - - -
481B SER* 2.6 29.5 + - - +
483B PHE* 3.2 21.8 - - - -
486C ASN* 2.6 22.4 + - - +
487C ILE* 3.4 4.6 + - - +
488C GLU 3.3 0.4 - - - -
489C ASP* 1.3 73.8 - - - +
491C LEU* 1.3 64.8 + - - +
494C TRP* 3.4 12.6 - - - +
497C VAL* 3.3 15.3 - - + +
401F LYS* 2.6 35.3 + - - +
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 3.7 29.4 - - + -
483B PHE* 4.8 1.6 - - + -
487C ILE* 3.0 32.8 + - + +
488C GLU* 3.8 5.8 - - + +
490C ASN* 1.3 78.7 - - - +
492C LEU* 1.3 63.2 + - - +
494C TRP* 4.1 2.4 - - - -
521C LEU* 3.6 24.7 - - + +
522C GLY* 3.3 27.5 - - - +
525C PHE* 3.7 33.9 - - + -
591C PHE* 3.8 12.8 - - + -
594C MET* 4.8 3.8 - - - -
596C LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C GLU 2.9 22.3 + - - +
489C ASP* 4.5 0.7 - - - +
491C LEU* 1.3 77.5 - - - +
493C SER* 1.3 66.2 + - - +
494C TRP* 3.8 5.9 - - - -
522C GLY 4.7 3.0 - - - +
525C PHE* 3.6 22.0 - - + -
526C LYS* 4.0 23.2 - - + +
529C ARG* 3.7 26.7 - - - +
614C ARG* 4.4 11.2 - - - +
374F ILE* 3.7 51.8 - - + +
375F GLY* 3.8 10.8 - - - +
380F ARG* 5.2 3.8 + - - -
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ASP* 3.0 21.7 + - - +
492C LEU* 1.3 87.6 - - - +
494C TRP* 1.3 68.5 + - - -
495C GLU* 2.7 38.8 + - - +
496C GLN* 3.3 28.0 + - - -
614C ARG* 5.3 2.4 + - - -
374F ILE* 4.5 16.1 - - - +
380F ARG* 4.3 1.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il